Founded in 1997, the MPO made its debut concert on 17 August 1998 under the direction of its first music director and founder, Kees Bakels.

Claus Peter Flor was the MPO's music director, starting from August 2008, with an initial contract of 3 years.

Dato' Seri Ooi Chean See was the founding Resident Conductor of the Malaysian Philharmonic Orchestra from 1998 until 2006.

Naohisa Furusawa, a member of the MPO double bass section since January 2003, was named Resident Conductor in 2016.

Seven out of the nine musicians who received the non-renewal notices filed a legal suit against the MPO at the Malaysian Industrial Court, challenging their former employer's decision not to extend their contracts.

[4][5] In a separate case, in May 2014, the Malaysian Industrial Court had ordered the MPO to pay a fine of US$147,000 for the dismissal of its former General Manager, Kim Sargeant in 2006 This decision was reversed in 2016.